look like eclipse bug but initially I report about it here:

0) I was trying to find the reason of https://jira.jboss.org/jira/browse/JBIDE-5889; dvdstore-ejb was opened successfully;
1) close JBDS;
2) run JBDS;
3) try to open Open dvdstore-ejb - stacktrace:

java.lang.NullPointerException
at org.eclipse.emf.common.notify.impl.BasicNotifierImpl.eNotify(BasicNotifierImpl.java:280)
at org.eclipse.emf.common.notify.impl.NotifyingListImpl.dispatchNotification(NotifyingListImpl.java:267)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl$SynchronizedResourcesEList.dispatchNotification(ProjectResourceSetImpl.java:335)
at org.eclipse.emf.common.notify.impl.NotifyingListImpl.addUnique(NotifyingListImpl.java:300)
at org.eclipse.emf.common.util.AbstractEList.add(AbstractEList.java:307)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl$SynchronizedResourcesEList.add(ProjectResourceSetImpl.java:81)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl.createResource(ProjectResourceSetImpl.java:392)
at org.eclipse.wst.common.internal.emfworkbench.integration.ProjectResourceSetEditImpl.createResource(ProjectResourceSetEditImpl.java:48)
at org.eclipse.emf.ecore.resource.impl.ResourceSetImpl.demandCreateResource(ResourceSetImpl.java:239)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl.getResource(ProjectResourceSetImpl.java:693)
at org.eclipse.jst.jee.model.internal.JEE5ModelProvider.getModelResource(JEE5ModelProvider.java:155)
at org.eclipse.jst.jee.model.internal.EAR5ModelProvider.getModelObject(EAR5ModelProvider.java:50)
at org.eclipse.jst.j2ee.project.EarUtilities.getEARLibDir(EarUtilities.java:372)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.getBaseEARLibRefs(J2EEComponentClasspathContainer.java:321)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.update(J2EEComponentClasspathContainer.java:211)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.install(J2EEComponentClasspathContainer.java:351)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathInitializer.initialize(J2EEComponentClasspathInitializer.java:47)
at org.eclipse.jdt.internal.core.JavaModelManager.initializeContainer(JavaModelManager.java:2642)
at org.eclipse.jdt.internal.core.JavaModelManager.getClasspathContainer(JavaModelManager.java:1813)
at org.eclipse.jdt.core.JavaCore.getClasspathContainer(JavaCore.java:2652)
at org.eclipse.jdt.launching.JavaRuntime.computeUnresolvedRuntimeClasspath(JavaRuntime.java:752)
at org.eclipse.jdt.launching.StandardClasspathProvider.computeUnresolvedClasspath(StandardClasspathProvider.java:48)
at org.eclipse.jdt.launching.JavaRuntime.computeUnresolvedRuntimeClasspath(JavaRuntime.java:1191)
at org.hibernate.eclipse.console.utils.ClassLoaderHelper.getClasspath(ClassLoaderHelper.java:146)
at org.hibernate.eclipse.console.EclipseLaunchConsoleConfigurationPreferences.getCustomClassPathURLS(EclipseLaunchConsoleConfigurationPreferences.java:95)
at org.hibernate.console.ConsoleConfiguration.getCustomClassPathURLs(ConsoleConfiguration.java:242)
at org.hibernate.console.ConsoleConfiguration.createClassLoader(ConsoleConfiguration.java:277)
at org.hibernate.console.ConsoleConfiguration.buildWith(ConsoleConfiguration.java:316)
at org.hibernate.console.ConsoleConfiguration.build(ConsoleConfiguration.java:147)
at org.hibernate.eclipse.console.workbench.ConsoleConfigurationWorkbenchAdapter.getChildren(ConsoleConfigurationWorkbenchAdapter.java:40)
at org.hibernate.eclipse.console.workbench.BasicWorkbenchAdapter.getChildren(BasicWorkbenchAdapter.java:100)
at org.hibernate.eclipse.console.workbench.BasicWorkbenchAdapter.fetchDeferredChildren(BasicWorkbenchAdapter.java:106)
at org.eclipse.ui.progress.DeferredTreeContentManager$1.run(DeferredTreeContentManager.java:234)
at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)

4) try to Edit dvdstore-ejb - stacktrace:

Unhandled event loop exception

java.lang.NullPointerException
at org.eclipse.emf.common.notify.impl.BasicNotifierImpl.eNotify(BasicNotifierImpl.java:280)
at org.eclipse.emf.common.notify.impl.NotifyingListImpl.dispatchNotification(NotifyingListImpl.java:267)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl$SynchronizedResourcesEList.dispatchNotification(ProjectResourceSetImpl.java:335)
at org.eclipse.emf.common.notify.impl.NotifyingListImpl.addUnique(NotifyingListImpl.java:300)
at org.eclipse.emf.common.util.AbstractEList.add(AbstractEList.java:307)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl$SynchronizedResourcesEList.add(ProjectResourceSetImpl.java:81)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl.createResource(ProjectResourceSetImpl.java:392)
at org.eclipse.wst.common.internal.emfworkbench.integration.ProjectResourceSetEditImpl.createResource(ProjectResourceSetEditImpl.java:48)
at org.eclipse.emf.ecore.resource.impl.ResourceSetImpl.demandCreateResource(ResourceSetImpl.java:239)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl.getResource(ProjectResourceSetImpl.java:693)
at org.eclipse.jst.jee.model.internal.JEE5ModelProvider.getModelResource(JEE5ModelProvider.java:155)
at org.eclipse.jst.jee.model.internal.EAR5ModelProvider.getModelObject(EAR5ModelProvider.java:50)
at org.eclipse.jst.j2ee.project.EarUtilities.getEARLibDir(EarUtilities.java:372)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.getBaseEARLibRefs(J2EEComponentClasspathContainer.java:321)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.update(J2EEComponentClasspathContainer.java:211)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.install(J2EEComponentClasspathContainer.java:351)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathInitializer.initialize(J2EEComponentClasspathInitializer.java:47)
at org.eclipse.jdt.internal.core.JavaModelManager.initializeContainer(JavaModelManager.java:2642)
at org.eclipse.jdt.internal.core.JavaModelManager.getClasspathContainer(JavaModelManager.java:1813)
at org.eclipse.jdt.core.JavaCore.getClasspathContainer(JavaCore.java:2652)
at org.eclipse.jdt.launching.JavaRuntime.computeUnresolvedRuntimeClasspath(JavaRuntime.java:752)
at org.eclipse.jdt.launching.StandardClasspathProvider.computeUnresolvedClasspath(StandardClasspathProvider.java:48)
at org.eclipse.jdt.launching.JavaRuntime.computeUnresolvedRuntimeClasspath(JavaRuntime.java:1191)
at org.eclipse.jdt.debug.ui.launchConfigurations.JavaClasspathTab.createClasspathModel(JavaClasspathTab.java:254)
at org.eclipse.jdt.debug.ui.launchConfigurations.JavaClasspathTab.refresh(JavaClasspathTab.java:242)
at org.eclipse.jdt.debug.ui.launchConfigurations.JavaClasspathTab.initializeFrom(JavaClasspathTab.java:197)
at org.hibernate.eclipse.launch.ConsoleConfigurationJavaClasspathTab.initializeFrom(ConsoleConfigurationJavaClasspathTab.java:57)
at org.eclipse.debug.ui.AbstractLaunchConfigurationTabGroup.initializeFrom(AbstractLaunchConfigurationTabGroup.java:86)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationTabGroupWrapper.initializeFrom(LaunchConfigurationTabGroupWrapper.java:194)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationTabGroupViewer.displayInstanceTabs(LaunchConfigurationTabGroupViewer.java:802)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationTabGroupViewer$8.run(LaunchConfigurationTabGroupViewer.java:678)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationTabGroupViewer.inputChanged(LaunchConfigurationTabGroupViewer.java:695)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationTabGroupViewer.setInput0(LaunchConfigurationTabGroupViewer.java:657)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationTabGroupViewer.setInput(LaunchConfigurationTabGroupViewer.java:633)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationPropertiesDialog.initializeContent(LaunchConfigurationPropertiesDialog.java:126)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationsDialog.createContents(LaunchConfigurationsDialog.java:425)
at org.eclipse.jface.window.Window.create(Window.java:431)
at org.eclipse.jface.dialogs.Dialog.create(Dialog.java:1089)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationsDialog.create(LaunchConfigurationsDialog.java:354)
at org.eclipse.jface.window.Window.open(Window.java:790)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationsDialog.open(LaunchConfigurationsDialog.java:1065)
at org.eclipse.debug.internal.ui.launchConfigurations.LaunchConfigurationPropertiesDialog.open(LaunchConfigurationPropertiesDialog.java:227)
at org.eclipse.debug.ui.DebugUITools.openLaunchConfigurationPropertiesDialog(DebugUITools.java:448)
at org.eclipse.debug.ui.DebugUITools.openLaunchConfigurationPropertiesDialog(DebugUITools.java:425)
at org.hibernate.eclipse.console.actions.EditConsoleConfiguration.edit(EditConsoleConfiguration.java:88)
at org.hibernate.eclipse.console.actions.EditConsoleConfiguration.doRun(EditConsoleConfiguration.java:68)
at org.hibernate.eclipse.console.actions.ConsoleConfigurationBasedAction.run(ConsoleConfigurationBasedAction.java:65)
at org.eclipse.ui.actions.BaseSelectionListenerAction.runWithEvent(BaseSelectionListenerAction.java:168)
at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584)
at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501)
at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:411)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1003)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3910)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3503)
at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2405)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2369)
at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2221)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:500)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:493)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:113)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:194)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:368)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:559)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:514)
at org.eclipse.equinox.launcher.Main.run(Main.java:1311)
at org.eclipse.equinox.launcher.Main.main(Main.java:1287)

5) try to create new console config:

java.lang.NullPointerException
at org.eclipse.emf.common.notify.impl.BasicNotifierImpl.eNotify(BasicNotifierImpl.java:280)
at org.eclipse.emf.common.notify.impl.NotifyingListImpl.dispatchNotification(NotifyingListImpl.java:267)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl$SynchronizedResourcesEList.dispatchNotification(ProjectResourceSetImpl.java:335)
at org.eclipse.emf.common.notify.impl.NotifyingListImpl.addUnique(NotifyingListImpl.java:300)
at org.eclipse.emf.common.util.AbstractEList.add(AbstractEList.java:307)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl$SynchronizedResourcesEList.add(ProjectResourceSetImpl.java:81)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl.createResource(ProjectResourceSetImpl.java:392)
at org.eclipse.wst.common.internal.emfworkbench.integration.ProjectResourceSetEditImpl.createResource(ProjectResourceSetEditImpl.java:48)
at org.eclipse.emf.ecore.resource.impl.ResourceSetImpl.demandCreateResource(ResourceSetImpl.java:239)
at org.eclipse.jem.internal.util.emf.workbench.ProjectResourceSetImpl.getResource(ProjectResourceSetImpl.java:693)
at org.eclipse.jst.jee.model.internal.JEE5ModelProvider.getModelResource(JEE5ModelProvider.java:155)
at org.eclipse.jst.jee.model.internal.EAR5ModelProvider.getModelObject(EAR5ModelProvider.java:50)
at org.eclipse.jst.j2ee.project.EarUtilities.getEARLibDir(EarUtilities.java:372)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.getBaseEARLibRefs(J2EEComponentClasspathContainer.java:321)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.update(J2EEComponentClasspathContainer.java:211)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathContainer.install(J2EEComponentClasspathContainer.java:351)
at org.eclipse.jst.j2ee.internal.common.classpath.J2EEComponentClasspathInitializer.initialize(J2EEComponentClasspathInitializer.java:47)
at org.eclipse.jdt.internal.core.JavaModelManager.initializeContainer(JavaModelManager.java:2642)
at org.eclipse.jdt.internal.core.JavaModelManager.getClasspathContainer(JavaModelManager.java:1813)
at org.eclipse.jdt.core.JavaCore.getClasspathContainer(JavaCore.java:2652)
at org.eclipse.jdt.launching.JavaRuntime.computeUnresolvedRuntimeClasspath(JavaRuntime.java:752)
at org.eclipse.jdt.launching.StandardClasspathProvider.computeUnresolvedClasspath(StandardClasspathProvider.java:48)
at org.eclipse.jdt.launching.JavaRuntime.computeUnresolvedRuntimeClasspath(JavaRuntime.java:1191)
at org.hibernate.eclipse.launch.ConsoleConfigurationJavaClasspathTab.isValid(ConsoleConfigurationJavaClasspathTab.java:37)
at org.hibernate.eclipse.console.wizards.ConsoleConfigurationWizardPage.dialogChanged(ConsoleConfigurationWizardPage.java:279)
at org.hibernate.eclipse.console.wizards.ConsoleConfigurationWizardPage$1.modifyText(ConsoleConfigurationWizardPage.java:198)
at org.eclipse.swt.widgets.TypedListener.handleEvent(TypedListener.java:167)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1003)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1027)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1008)
at org.eclipse.swt.widgets.Text.wmCommandChild(Text.java:2526)
at org.eclipse.swt.widgets.Control.WM_COMMAND(Control.java:4082)
at org.eclipse.swt.widgets.Control.windowProc(Control.java:3949)
at org.eclipse.swt.widgets.Display.windowProc(Display.java:4632)
at org.eclipse.swt.internal.win32.OS.CallWindowProcW(Native Method)
at org.eclipse.swt.internal.win32.OS.CallWindowProc(OS.java:2314)
at org.eclipse.swt.widgets.Text.callWindowProc(Text.java:255)
at org.eclipse.swt.widgets.Control.windowProc(Control.java:4036)
at org.eclipse.swt.widgets.Text.windowProc(Text.java:2170)
at org.eclipse.swt.widgets.Display.windowProc(Display.java:4619)
at org.eclipse.swt.internal.win32.OS.DispatchMessageW(Native Method)
at org.eclipse.swt.internal.win32.OS.DispatchMessage(OS.java:2411)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3501)
at org.eclipse.jface.window.Window.runEventLoop(Window.java:825)
at org.eclipse.jface.window.Window.open(Window.java:801)
at org.eclipse.ui.internal.actions.NewWizardShortcutAction.run(NewWizardShortcutAction.java:135)
at org.eclipse.jface.action.Action.runWithEvent(Action.java:498)
at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:584)
at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:501)
at org.eclipse.jface.action.ActionContributionItem$5.handleEvent(ActionContributionItem.java:411)
at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84)
at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1003)
at org.eclipse.swt.widgets.Display.runDeferredEvents(Display.java:3910)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3503)
at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2405)
at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2369)
at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2221)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:500)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:493)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:113)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:194)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:368)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:559)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:514)
at org.eclipse.equinox.launcher.Main.run(Main.java:1311)
at org.eclipse.equinox.launcher.Main.main(Main.java:1287)